It currently seems not to be possible to assign one contact to more than
one account. Can/will this be changed?

Probably not in the near future. Currently you can achieve this by
adding your contacts separately and then merging them in a single meta
contact.

How can I find out to which account a contact belongs?

Hover above it then check the icon that appears in the tooltip. It
identifies the protocol and in case you have several accounts of that
protocol it should also come with an index that would help you determine
which one the contact is coming from.

Deleting contacts is problematic. I often have seen the situation that
such contacts neither disappear nor do I see anything relevant in the log.